10.25386/genetics.6007730.v2 Timthy P. Bilton Timthy P. Bilton John C. McEwan John C. McEwan Shannon M. Clarke Shannon M. Clarke Rudiger Brauning Rudiger Brauning Tracey C. van Stijn Tracey C. van Stijn Suzanne J. Rowe Suzanne J. Rowe Ken G. Dodds Ken G. Dodds Supplemental Material for Bilton et al., 2018 GSA Journals 2018 genotyping-by-sequencing linkage disequilibrium maximum likelihood allelic dropout low coverage Genetics 2018-07-13 19:40:31 Dataset https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Bilton_et_al_2018_in_review_/6007730 Scripts for generating the simulated sequencing data are provided in File S1. Figures S1 and S2 gives bias and standard errors of LD estimates for the second and third simulation scenarios. Figure~S3 gives the standard errors of the allele frequency estimates for all the simulations. Figures S4 and S5 gives the mean square errors of LD estimates for the second and third simulation scenarios. Figure S6 gives the mean read depth distribution for the SNPs used in the deer dataset and Figure S7 gives the distribution of the sequencing error estimates for the deer analysis.